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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: May 14, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

BION web server: predicting non-specifically bound surface ions.

Marharyta Petukh1, Taylor Kimmet, Emil Alexov

  • 1Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.

Bioinformatics (Oxford, England)
|February 6, 2013
PubMed
Summary
This summary is machine-generated.

Predicting loosely bound ions on protein surfaces is challenging. The BION web server offers a user-friendly tool to identify these surface-bound ions, aiding in biophysical modeling.

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Last Updated: May 14, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Capturing the Interaction Kinetics of an Ion Channel Protein with Small Molecules by the Bio-layer Interferometry Assay
10:41

Capturing the Interaction Kinetics of an Ion Channel Protein with Small Molecules by the Bio-layer Interferometry Assay

Published on: March 7, 2018

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Ions are crucial cellular components that bind to macromolecules like proteins.
  • Ion-protein interactions significantly influence protein biophysical properties, essential for accurate modeling.
  • Experimental determination of loosely bound ion positions on protein surfaces remains difficult.

Purpose of the Study:

  • To develop a computational tool for predicting surface-bound ions on proteins.
  • To provide an accessible web server for researchers needing to identify ion binding sites.

Main Methods:

  • Development of the BION web server.
  • Utilizes protein coordinate files as input.
  • Predicts surface-bound ions where specific interactions are not dominant.

Main Results:

  • The BION web server successfully predicts surface-bound ions.
  • The server provides an easy-to-use interface requiring only a coordinate file.
  • Predicted ion-bound coordinates are displayed and downloadable.

Conclusions:

  • The BION web server addresses the need for tools predicting difficult-to-determine surface-bound ions.
  • This tool facilitates more accurate biophysical modeling by accounting for ion binding.
  • The server offers a practical solution for researchers studying ion-macromolecule interactions.